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Changes to existing functions:
- get_lfc_celltype: removed expression_pct parameter, replaced with ... where arguments can directly be provided to Seurat::FindMarkers
- get_ligand_signaling_path: added minmax_scaling parameter to scale the weights of signaling and regulatory networks
- make*_heatmap_ggplot: returned plot no longer replaces hyphens with dots
- make_mushroom_plot: additional ... parameter to pass arguments to ggplot2::theme
- make_circos_lr: added separate_legend parameter to determine whether the plot and legend are returned as separate objects
- Added nsga2R optimization functions, renamed old model evaluation functions of mlrMBO
- calculate_de: default values changed from NA to NULL
- get_exprs_avg: default values changed from NA to NULL; additional ... parameter to pass arguments to Seurat::AverageExpression
- generate_prioritization_tables: added scenario parameter
Revised vignettes for readability
parameter_optimization vignette now contains code on how to submit the job to a computing cluster
Added new vignette on using LIANA to construct the lignad-receptor network part of the prior model